Get contourf image as array

I've been searching and reading through source code and google searches to see if this is possible, but no luck so far. I'm basically trying to map some data using Basemap, use contourf to map it to an image, and then put that image in a geotiff (or other format) for use in other GIS programs. I have other tools for remapping data and creating geotiffs, but the contour image looks better. All I would need to get this to work would be an array representing the image inside the axes of a contourf plot. I found a lot of geotiff -> Basemap png results, but I would like the reverse.

Since the plots are made using paths/patches I'm guessing I would have to have a backend render the image and then extract the image somehow. Does anyone have some tips or tricks to do something like this? Or am I thinking about this completely wrong?

Thanks for any help and if you could CC me in any replies it would be much appreciated.

-Dave

pardon the query if it seems dumb, but why don’t you do a savefig()

after plotting the data and then convert it to any format you like?

alternatively, contour() and contourf() both create paths that can
be accessed:

cf = contourf(…)

output = cf.collections.pop()

paths = output.get_paths()[i] # for the various contours

the x,y coordinates can then be accessed as

xcoords = paths.vertices.transpose()[0]

ycoords = paths.vertices.transpose()[1]

you can then do whatever you wish with them.

Joy

···

On Wed, Oct 15, 2014 at 9:11 PM, David Hoese <dhoese@…287…> wrote:

I’ve been searching and reading through source code and google searches

to see if this is possible, but no luck so far. I’m basically trying to

map some data using Basemap, use contourf to map it to an image, and

then put that image in a geotiff (or other format) for use in other GIS

programs. I have other tools for remapping data and creating geotiffs,

but the contour image looks better. All I would need to get this to work

would be an array representing the image inside the axes of a contourf

plot. I found a lot of geotiff -> Basemap png results, but I would like

the reverse.

Since the plots are made using paths/patches I’m guessing I would have

to have a backend render the image and then extract the image somehow.

Does anyone have some tips or tricks to do something like this? Or am I

thinking about this completely wrong?

Thanks for any help and if you could CC me in any replies it would be

much appreciated.

-Dave


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tasks and completes his affairs,
the people say
“It all happened naturally”

                                     - Te Tao Ch'ing

For the first question, if I save the figure (as a PNG I'm guessing, unless you can save into a more array-like format), I'd have to make sure that there were no labels or ticks and that the axes fit the whole figure. I'd also have to get the dpi and size information correct, but I suppose it would be possible that way. I was hoping for something a little easier and in-memory. This might be the simplest answer the more I think about it.

If I'm starting from the paths, I'd still have to write them to the "grid" array. I thought maybe the backend could do that and I magically get the image.

I'll look in to using savefig and getting the data out.

-Dave

···

On 10/15/14, 12:42 PM, Joy merwin monteiro wrote:

pardon the query if it seems dumb, but why don't you do a savefig()
after plotting the data and then convert it to any format you like?

alternatively, contour() and contourf() both create paths that can
be accessed:

cf = contourf(.....)

output = cf.collections.pop()
paths = output.get_paths()[i] # for the various contours

the x,y coordinates can then be accessed as

xcoords = paths.vertices.transpose()[0]
ycoords = paths.vertices.transpose()[1]

you can then do whatever you wish with them.

Joy

On Wed, Oct 15, 2014 at 9:11 PM, David Hoese <dhoese@…287… > <mailto:dhoese@…287…>> wrote:

    I've been searching and reading through source code and google searches
    to see if this is possible, but no luck so far. I'm basically trying to
    map some data using Basemap, use contourf to map it to an image, and
    then put that image in a geotiff (or other format) for use in other GIS
    programs. I have other tools for remapping data and creating geotiffs,
    but the contour image looks better. All I would need to get this to work
    would be an array representing the image inside the axes of a contourf
    plot. I found a lot of geotiff -> Basemap png results, but I would like
    the reverse.

    Since the plots are made using paths/patches I'm guessing I would have
    to have a backend render the image and then extract the image somehow.
    Does anyone have some tips or tricks to do something like this? Or am I
    thinking about this completely wrong?

    Thanks for any help and if you could CC me in any replies it would be
    much appreciated.

    -Dave

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--
The best ruler, when he finishes his
tasks and completes his affairs,
the people say
“It all happened naturally”

                                          - Te Tao Ch'ing

What you are looking for is called “rasterization”. Matplotlib does this deep within the codebase and is not accessible (believe me, I tried). However, there have been other discussions in this mailing list about how to use GDAL to rasterize a set of polygons (represented as paths), including some links to stack-overflow questions. It isn’t a complete end-to-end solution, but the pieces are there.

Cheers!
Ben Root

···

On Wed, Oct 15, 2014 at 2:09 PM, David Hoese <dhoese@…1003…7…> wrote:

For the first question, if I save the figure (as a PNG I’m guessing,

unless you can save into a more array-like format), I’d have to make

sure that there were no labels or ticks and that the axes fit the whole

figure. I’d also have to get the dpi and size information correct, but I

suppose it would be possible that way. I was hoping for something a

little easier and in-memory. This might be the simplest answer the more

I think about it.

If I’m starting from the paths, I’d still have to write them to the

“grid” array. I thought maybe the backend could do that and I magically

get the image.

I’ll look in to using savefig and getting the data out.

-Dave

On 10/15/14, 12:42 PM, Joy merwin monteiro wrote:

pardon the query if it seems dumb, but why don’t you do a savefig()

after plotting the data and then convert it to any format you like?

alternatively, contour() and contourf() both create paths that can

be accessed:

cf = contourf(…)

output = cf.collections.pop()

paths = output.get_paths()[i] # for the various contours

the x,y coordinates can then be accessed as

xcoords = paths.vertices.transpose()[0]

ycoords = paths.vertices.transpose()[1]

you can then do whatever you wish with them.

Joy

On Wed, Oct 15, 2014 at 9:11 PM, David Hoese <dhoese@…287…

mailto:dhoese@...287...> wrote:

I've been searching and reading through source code and google searches
to see if this is possible, but no luck so far. I'm basically trying to
map some data using Basemap, use contourf to map it to an image, and
then put that image in a geotiff (or other format) for use in other GIS
programs. I have other tools for remapping data and creating geotiffs,
but the contour image looks better. All I would need to get this to work
would be an array representing the image inside the axes of a contourf
plot. I found a lot of geotiff -> Basemap png results, but I would like
the reverse.
Since the plots are made using paths/patches I'm guessing I would have
to have a backend render the image and then extract the image somehow.
Does anyone have some tips or tricks to do something like this? Or am I
thinking about this completely wrong?
Thanks for any help and if you could CC me in any replies it would be
much appreciated.
-Dave
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The best ruler, when he finishes his

tasks and completes his affairs,

the people say

“It all happened naturally”

                                      - Te Tao Ch'ing

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Thanks Ben. I'll take a look through the archive.

···

On 10/16/14, 9:43 AM, Benjamin Root wrote:

What you are looking for is called "rasterization". Matplotlib does this
deep within the codebase and is not accessible (believe me, I tried).
However, there have been other discussions in this mailing list about
how to use GDAL to rasterize a set of polygons (represented as paths),
including some links to stack-overflow questions. It isn't a complete
end-to-end solution, but the pieces are there.

Cheers!
Ben Root

On Wed, Oct 15, 2014 at 2:09 PM, David Hoese <dhoese@…287… > <mailto:dhoese@…287…>> wrote:

    For the first question, if I save the figure (as a PNG I'm guessing,
    unless you can save into a more array-like format), I'd have to make
    sure that there were no labels or ticks and that the axes fit the whole
    figure. I'd also have to get the dpi and size information correct, but I
    suppose it would be possible that way. I was hoping for something a
    little easier and in-memory. This might be the simplest answer the more
    I think about it.

    If I'm starting from the paths, I'd still have to write them to the
    "grid" array. I thought maybe the backend could do that and I magically
    get the image.

    I'll look in to using savefig and getting the data out.

    -Dave

    On 10/15/14, 12:42 PM, Joy merwin monteiro wrote:
    > pardon the query if it seems dumb, but why don't you do a savefig()
    > after plotting the data and then convert it to any format you like?
    >
    > alternatively, contour() and contourf() both create paths that can
    > be accessed:
    >
    > cf = contourf(…)
    >
    > output = cf.collections.pop()
    > paths = output.get_paths()[i] # for the various contours
    >
    > the x,y coordinates can then be accessed as
    >
    > xcoords = paths.vertices.transpose()[0]
    > ycoords = paths.vertices.transpose()[1]
    >
    > you can then do whatever you wish with them.
    >
    > Joy
    >
    > On Wed, Oct 15, 2014 at 9:11 PM, David Hoese <dhoese@…287… <mailto:dhoese@…287…> > > <mailto:dhoese@…287…>> wrote:
     >
     > I've been searching and reading through source code and
    google searches
     > to see if this is possible, but no luck so far. I'm basically
    trying to
     > map some data using Basemap, use contourf to map it to an
    image, and
     > then put that image in a geotiff (or other format) for use in
    other GIS
     > programs. I have other tools for remapping data and creating
    geotiffs,
     > but the contour image looks better. All I would need to get
    this to work
     > would be an array representing the image inside the axes of a
    contourf
     > plot. I found a lot of geotiff -> Basemap png results, but I
    would like
     > the reverse.
     >
     > Since the plots are made using paths/patches I'm guessing I
    would have
     > to have a backend render the image and then extract the image
    somehow.
     > Does anyone have some tips or tricks to do something like
    this? Or am I
     > thinking about this completely wrong?
     >
     > Thanks for any help and if you could CC me in any replies it
    would be
     > much appreciated.
     >
     > -Dave
     >
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     > Monitor 10 servers for $9/Month.
     > Get alerted through email, SMS, voice calls or mobile push
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     > _______________________________________________
     > Matplotlib-users mailing list
     > Matplotlib-users@lists.sourceforge.net
    <mailto:Matplotlib-users@lists.sourceforge.net>
     > <mailto:Matplotlib-users@lists.sourceforge.net
    <mailto:Matplotlib-users@lists.sourceforge.net>>
     > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
     >
     > –
     > The best ruler, when he finishes his
     > tasks and completes his affairs,
     > the people say
     > “It all happened naturally”
     >
     > - Te Tao Ch'ing

    ------------------------------------------------------------------------------
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